Gianluca Matera     email
Institute for Molecular Infection Biology

Prof. Dr. Jörg Vogel (Würzburg)
Promotion Committee:
Prof. Dr. Jörg Vogel (Würzburg)
Prof. Dr. Kai Papenfort (München)
Dr. Franziska Faber (Würzburg)

Unveiling the Hfq mediated RNA-RNA interactome of Salmonella Typihmurium

In recent decades, new insights into post-transcriptional regulation has been of central importance for uncovering new ways prokaryotes fine tune gene expression. In particular, bacterial pathogens have proved to take advantage of such ribo-regulation to establish successful infection inside the host cell (Westermann et al. 2016, Nature [1]).

In the two well-established bacterial models, Escherichia coli and Salmonella Typhimurium, this regulation mainly occurs through the cooperation of RNA chaperones, as Hfq and ProQ, and their partner small RNAs (sRNAs). By direct base pairing with the target mRNAs, sRNAs are able to regulate gene expression. 

One of the big challenges in studying sRNA-mediated regulation is identifying their target RNAs. Recent studies showed how this can be achieved using high throughput RNA-sequencing technologies, e.g. RIL-seq or CLASH (Melamed et al. 2016, Mol Cell [2]; Waters et al. 2017, EMBO J [3]), overcoming the need of only relying on bioinformatics tools predictions.

My PhD project aims to apply previously cited methods to identify the Hfq mediated RNA-RNA interactome in the human pathogen Salmonella Typhimurium. The methods will be applied in different growth conditions to produce a high-resolution map of the Hfq-interactome rewiring. Eventually, an interesting challenge will be to extend the methods to Salmonella-infected cell lines to capture the Hfq-sRNA interactome at different time points during infection. Taken together, my experiments will provide useful insights into the complex post-transcriptional regulation of a pathogenic bacteria.


[1] Westermann AJ, Förstner KU, Amman F, et al. Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Nature. 2016;529(7587):496-501. doi:10.1038/nature16547.

[2] Melamed S, Peer A, Faigennbaum-Romm R, et al. Global Mapping of Small RNA-Target Interactions in Bacteria. Molecular Cell. 2016;63(5):884-97.  doi:10.1016/j.molcel.2016.07.026

[3] Waters SA, Mcateer SP, Kudla G, et al. Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E. The EMBO Journal. 2016;36(3):374-387. doi:10.15252/embj.201694639.